BACKGROUND: Internet-based cognitive behavioral therapy (iCBT) is a promising new treatment method for depression and anxiety. However, it is important to determine whether its results can be replicated in routine care before its implementation on a large scale. Although many studies have demonstrated the efficacy of iCBT under controlled conditions, only a few studies have investigated its effectiveness in routine care. Furthermore, several effects of iCBT such as treatment effects in routine care are unclear. OBJECTIVE: This study aimed to evaluate the clinical effectiveness of iCBT for depression and anxiety in routine secondary care. METHODS: n a retrospective cohort study, we analysed patients treated for depression or anxiety in a dedicated iCBT clinic in secondary care in Denmark. Patients were examined before treatment and weekly thereafter by using the Patient Health Questionnaire-9 and the Generalized Anxiety Disorder-7 scales for the diagnoses of depression and anxiety, respectively. Primary analyses were conducted using a linear mixed-effects model with random slope and intercept. Secondary analyses were conducted using baseline characteristics as predictors (gender, age, highest level of education, occupational status, marital status, psychotropic medication use, consumption of alcohol, and leisure drugs). Additionally, logistic regression analyses were used to predict noncompletion of treatment. RESULTS: A total of 203 (depression, N=60; anxiety, N=143) patients were included. Participants were mainly female (78.3% with depression and 65.7% with anxiety), with a mean age of 36.03 (SD 10.97) years (range, 19-67 years) for patients with depression and 36.80 (SD 13.55) years (range, 19-69 years) for patients with anxiety. The completion rates were 62% (37) and 40% (57) for depression and anxiety treatments, respectively. The primary analyses revealed large and significant reductions in the symptom levels of depression (beta=-6.27, SE 0.83, P<.001, d=1.0) and anxiety (beta=-3.78, SE 0.43, P<.001, d=1.1). High baseline severity of the primary disorder was associated with high treatment gains (r=-0.31 for depression; r=-0.41 for anxiety). In patients with anxiety, high baseline severity also predicted a high risk of noncompletion (odds ratio=1.08, CI=1.01-1.16, P=.03). An increase in the baseline severity of the comorbid disorder slightly increased the risk of noncompletion for both disorders (depression: odds ratio=1.03, CI=1.01-1.06, P=.02; anxiety: odds ratio=1.08, CI=1.01-1.16, P=.03). CONCLUSIONS: iCBT can be clinically effective in routine care. Since depression and anxiety are costly and debilitating disorders that are vastly undertreated, this finding is important. Additionally, iCBT may help bridge the gap between the need for treatment and its provision. Our results are comparable to the within-group results of efficacy and effectiveness studies. Our noncompletion rates are similar to those observed in psychotherapy but are higher than those reported in similar clinics. Multiple factors predicted outcome and noncompletion. However, all predictor effects were statistically weak.